It could be a rogue ninja from a hidden village who has a vendetta against the Green Beast. Maybe this antagonist blames the Green Beast for something that happened in the past.
Perhaps an evil organization that wants to use the Green Beast's power for their own malicious purposes. They might try to capture him and force him to use his abilities against Konoha. This organization could have some powerful and mysterious leaders with their own dark motives. They would send their minions after the Green Beast, creating a lot of action - packed chase scenes and battles in the fanfiction.
Maybe an alien from the Green Lantern universe who has a vendetta against the Green Lantern Corps decides to target Naruto's world. This alien believes that by causing chaos in the Naruto universe, he can draw out the Green Lanterns and destroy them. He has powerful weapons and abilities that are a challenge for Naruto and his friends to overcome.
Maybe an alien race that the Green Lanterns have underestimated. They see Naruto as an easy target since he's being neglected. But Naruto turns out to be more of a challenge than they thought. This alien race could have some sort of power that nullifies the Green Lantern rings, but Naruto's ninja skills are still effective against them.
It could be Orochimaru. He has always been interested in power and the secrets of the tailed beasts. He might see Naruto's transformation into a tailed beast as an opportunity to study and use that power for his own evil purposes. He could try to manipulate Naruto in his new state, perhaps by using genjutsu or other underhanded tactics.
In a crossover with Iron Man, Stark could be the main antagonist to the Green Goblin. Tony Stark would see the Goblin as a threat to the safety and order he wants to maintain in the world. He would use his high - tech suits and resources to try and stop the Green Goblin's chaos - causing ways.
It could be an envious witch. She was once in love with the prince (now the Beast) but he rejected her. So she cursed him and now she wants to make sure he never finds true love with the Dark Beauty.
The main antagonist could be the sorcerer who cast the spell on Belle to turn her into a beast. This sorcerer might have his own motives, like wanting to take over the village or the castle where Belle lives. He could be constantly trying to prevent Belle from finding a way to break the curse.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
A group of rogue ninja who are hunting nekoshou for their special powers could be the main antagonists. They see Naruto's newfound connection with the nekoshou as a threat and try to eliminate him and the nekoshou he is protecting.
It could be a corrupt ninja from within the village who wants Naruto out of the way. Maybe someone jealous of Naruto's popularity and power, so they frame him and get him sent to prison. This antagonist would then try to keep Naruto in prison by any means necessary.
Madara Uchiha could be a great antagonist. His powerful Sharingan abilities and his grand plans for the Naruto world would put him at odds with Supergirl. He might see her as a threat to his control and try to manipulate or defeat her. Another option could be Kaguya Otsutsuki. Her god - like powers and desire to reshape the world would clash with Supergirl's values and her attempts to protect the people of the Naruto universe.